Data Visualizatoin and Exploration v1
Joey Hulbert
9/19/2021
Running questions
- Below are some questions to revisit during further analysis
- Should we look at data from last decade only rather than last 30 years?
- How to structure this document
- climate variable (MAT, MAP)
- compare across symptoms (filtered?)
- compare across ‘number of unhealthy trees’
- compare across size class?
- compare across site type?
- climate variable (MAT, MAP)
Data Prep
Import data
Data downloaded manually from iNat.
Prepare dataset for extracting environmental data with climateNA
30 Normals
Import dataset with 30yr normals data
Merge data
Clean data
Add consistency to factors
Symptoms
## [1] "Branch Dieback or 'Flagging'"
## [2] "Browning Canopy"
## [3] "Extra Cone Crop"
## [4] "Healthy"
## [5] "Multiple Symptoms (please list in Notes)"
## [6] "New Dead Top (red or brown needles still attached)"
## [7] "Old Dead Top (needles already gone)"
## [8] "Other (please describe in Notes)"
## [9] "Thinning Canopy"
## [10] "Tree is dead"
## [11] "Yellowing Canopy"Unhealthy trees
## [1] "0" "1" "2-3" "4-6" "7-10"
## [6] "More than 10" "Not sure"Tree size
## [1] ""
## [2] "Large (too big to wrap arms around trunk)"
## [3] "Medium (can wrap arms around trunk)"
## [4] "No selection"
## [5] "Other"
## [6] "Small (can wrap hands around trunk)"
## [7] "Very Large (would take many people to wrap arms around trunk)"Filter data
Only include symptoms of interest
## [1] "Healthy"
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"
## [4] "Thinning Canopy"
## [5] "Tree is dead"Data Exploration
MAT
Symptoms
Site Severity
Size Class
MAP
Symptoms
AHM
Symptoms
SHM
Symptoms
Filtered SHM <200
MSP
Symptoms
CMD
Symptoms
Eref
Symptoms
Decade 2011-2020
Import dataset with Decade 2011-2020
Merge data
Clean data
Add consistency to factors
Symptoms
## [1] "Branch Dieback or 'Flagging'"
## [2] "Browning Canopy"
## [3] "Extra Cone Crop"
## [4] "Healthy"
## [5] "Multiple Symptoms (please list in Notes)"
## [6] "New Dead Top (red or brown needles still attached)"
## [7] "Old Dead Top (needles already gone)"
## [8] "Other (please describe in Notes)"
## [9] "Thinning Canopy"
## [10] "Tree is dead"
## [11] "Yellowing Canopy"Unhealthy trees
## [1] "0" "1" "2-3" "4-6" "7-10"
## [6] "More than 10" "Not sure"Tree size
## [1] ""
## [2] "Large (too big to wrap arms around trunk)"
## [3] "Medium (can wrap arms around trunk)"
## [4] "No selection"
## [5] "Other"
## [6] "Small (can wrap hands around trunk)"
## [7] "Very Large (would take many people to wrap arms around trunk)"Filter data
Only include symptoms of interest
## [1] "Healthy"
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"
## [4] "Thinning Canopy"
## [5] "Tree is dead"Data Exploration
MAT
Symptoms
Site Severity
Size Class
MAP
Symptoms
AHM
Symptoms
SHM
Symptoms
Filtered SHM <200
MSP
Symptoms
CMD
Symptoms
Eref
Symptoms
Large Trees on Severe sites
MSP
Symptoms
CMD
Symptoms
TOPO Data
Import TOPO Data
Merge data
Clean data
Add consistency to factors
Symptoms
## [1] "Branch Dieback or 'Flagging'"
## [2] "Browning Canopy"
## [3] "Extra Cone Crop"
## [4] "Healthy"
## [5] "Multiple Symptoms (please list in Notes)"
## [6] "New Dead Top (red or brown needles still attached)"
## [7] "Old Dead Top (needles already gone)"
## [8] "Other (please describe in Notes)"
## [9] "Thinning Canopy"
## [10] "Tree is dead"
## [11] "Yellowing Canopy"Unhealthy trees
## [1] "0" "1" "2-3" "4-6" "7-10"
## [6] "More than 10" "Not sure"Tree size
## [1] ""
## [2] "Large (too big to wrap arms around trunk)"
## [3] "Medium (can wrap arms around trunk)"
## [4] "No selection"
## [5] "Other"
## [6] "Small (can wrap hands around trunk)"
## [7] "Very Large (would take many people to wrap arms around trunk)"Filter data
Only include symptoms of interest
## [1] "Healthy"
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"
## [4] "Thinning Canopy"
## [5] "Tree is dead"Data Exploration
Aspect
Symptoms
## [1] "id"
## [2] "observed_on_string"
## [3] "observed_on"
## [4] "time_observed_at"
## [5] "time_zone"
## [6] "user_id"
## [7] "user_login"
## [8] "created_at"
## [9] "updated_at"
## [10] "quality_grade"
## [11] "license"
## [12] "url"
## [13] "image_url"
## [14] "sound_url"
## [15] "tag_list"
## [16] "description"
## [17] "num_identification_agreements"
## [18] "num_identification_disagreements"
## [19] "captive_cultivated"
## [20] "oauth_application_id"
## [21] "place_guess"
## [22] "latitude"
## [23] "longitude"
## [24] "positional_accuracy"
## [25] "private_place_guess"
## [26] "private_latitude"
## [27] "private_longitude"
## [28] "public_positional_accuracy"
## [29] "geoprivacy"
## [30] "taxon_geoprivacy"
## [31] "coordinates_obscured"
## [32] "positioning_method"
## [33] "positioning_device"
## [34] "place_town_name"
## [35] "place_county_name"
## [36] "place_state_name"
## [37] "place_country_name"
## [38] "place_admin1_name"
## [39] "place_admin2_name"
## [40] "species_guess"
## [41] "scientific_name"
## [42] "common_name"
## [43] "iconic_taxon_name"
## [44] "taxon_id"
## [45] "field.tree.canopy.symptoms"
## [46] "field.optional...did.the.tree.have.heat.damage"
## [47] "field.percent.canopy.affected...."
## [48] "field.number.of.additional.unhealthy.trees..of.same.species..in.area..within.sight."
## [49] "field.percent.of.trees..of.same.species..within.sight.that.are.unhealthy"
## [50] "field.other.factors...are.there.signs.or.symptoms.of.insect..diseases..or.other.damage."
## [51] "field.optional...what..other.factors..were.observed."
## [52] "field.optional...tree.size"
## [53] "field.optional...site.type"
## [54] "field.optional...site.location.description"
## [55] "field.optional...site.area.disturbance.level"
## [56] "field.optional...site.hydrology"
## [57] "field.optional...access.to.water"
## [58] "field.optional...slope.position"
## [59] "field.optional...were.there.any.other.unhealthy.plant.species.on.the.site."
## [60] "field.optional...timing.of.symptoms.estimate"
## [61] "field.optional...estimated.time.spent.to.make.this.observation....of.minutes."
## [62] "field.optional...can.we.follow.up.with.you."
## [63] "field.notes"
## [64] "X"
## [65] "Latitude"
## [66] "Longitude"
## [67] "Elevation"
## [68] "Tmax01"
## [69] "Tmax02"
## [70] "Tmax03"
## [71] "Tmax04"
## [72] "Tmax05"
## [73] "Tmax06"
## [74] "Tmax07"
## [75] "Tmax08"
## [76] "Tmax09"
## [77] "Tmax10"
## [78] "Tmax11"
## [79] "Tmax12"
## [80] "Tmin01"
## [81] "Tmin02"
## [82] "Tmin03"
## [83] "Tmin04"
## [84] "Tmin05"
## [85] "Tmin06"
## [86] "Tmin07"
## [87] "Tmin08"
## [88] "Tmin09"
## [89] "Tmin10"
## [90] "Tmin11"
## [91] "Tmin12"
## [92] "Tave01"
## [93] "Tave02"
## [94] "Tave03"
## [95] "Tave04"
## [96] "Tave05"
## [97] "Tave06"
## [98] "Tave07"
## [99] "Tave08"
## [100] "Tave09"
## [101] "Tave10"
## [102] "Tave11"
## [103] "Tave12"
## [104] "PPT01"
## [105] "PPT02"
## [106] "PPT03"
## [107] "PPT04"
## [108] "PPT05"
## [109] "PPT06"
## [110] "PPT07"
## [111] "PPT08"
## [112] "PPT09"
## [113] "PPT10"
## [114] "PPT11"
## [115] "PPT12"
## [116] "Rad01"
## [117] "Rad02"
## [118] "Rad03"
## [119] "Rad04"
## [120] "Rad05"
## [121] "Rad06"
## [122] "Rad07"
## [123] "Rad08"
## [124] "Rad09"
## [125] "Rad10"
## [126] "Rad11"
## [127] "Rad12"
## [128] "DD_0_01"
## [129] "DD_0_02"
## [130] "DD_0_03"
## [131] "DD_0_04"
## [132] "DD_0_05"
## [133] "DD_0_06"
## [134] "DD_0_07"
## [135] "DD_0_08"
## [136] "DD_0_09"
## [137] "DD_0_10"
## [138] "DD_0_11"
## [139] "DD_0_12"
## [140] "DD5_01"
## [141] "DD5_02"
## [142] "DD5_03"
## [143] "DD5_04"
## [144] "DD5_05"
## [145] "DD5_06"
## [146] "DD5_07"
## [147] "DD5_08"
## [148] "DD5_09"
## [149] "DD5_10"
## [150] "DD5_11"
## [151] "DD5_12"
## [152] "DD_18_01"
## [153] "DD_18_02"
## [154] "DD_18_03"
## [155] "DD_18_04"
## [156] "DD_18_05"
## [157] "DD_18_06"
## [158] "DD_18_07"
## [159] "DD_18_08"
## [160] "DD_18_09"
## [161] "DD_18_10"
## [162] "DD_18_11"
## [163] "DD_18_12"
## [164] "DD18_01"
## [165] "DD18_02"
## [166] "DD18_03"
## [167] "DD18_04"
## [168] "DD18_05"
## [169] "DD18_06"
## [170] "DD18_07"
## [171] "DD18_08"
## [172] "DD18_09"
## [173] "DD18_10"
## [174] "DD18_11"
## [175] "DD18_12"
## [176] "NFFD01"
## [177] "NFFD02"
## [178] "NFFD03"
## [179] "NFFD04"
## [180] "NFFD05"
## [181] "NFFD06"
## [182] "NFFD07"
## [183] "NFFD08"
## [184] "NFFD09"
## [185] "NFFD10"
## [186] "NFFD11"
## [187] "NFFD12"
## [188] "PAS01"
## [189] "PAS02"
## [190] "PAS03"
## [191] "PAS04"
## [192] "PAS05"
## [193] "PAS06"
## [194] "PAS07"
## [195] "PAS08"
## [196] "PAS09"
## [197] "PAS10"
## [198] "PAS11"
## [199] "PAS12"
## [200] "Eref01"
## [201] "Eref02"
## [202] "Eref03"
## [203] "Eref04"
## [204] "Eref05"
## [205] "Eref06"
## [206] "Eref07"
## [207] "Eref08"
## [208] "Eref09"
## [209] "Eref10"
## [210] "Eref11"
## [211] "Eref12"
## [212] "CMD01"
## [213] "CMD02"
## [214] "CMD03"
## [215] "CMD04"
## [216] "CMD05"
## [217] "CMD06"
## [218] "CMD07"
## [219] "CMD08"
## [220] "CMD09"
## [221] "CMD10"
## [222] "CMD11"
## [223] "CMD12"
## [224] "RH01"
## [225] "RH02"
## [226] "RH03"
## [227] "RH04"
## [228] "RH05"
## [229] "RH06"
## [230] "RH07"
## [231] "RH08"
## [232] "RH09"
## [233] "RH10"
## [234] "RH11"
## [235] "RH12"
## [236] "CMI01"
## [237] "CMI02"
## [238] "CMI03"
## [239] "CMI04"
## [240] "CMI05"
## [241] "CMI06"
## [242] "CMI07"
## [243] "CMI08"
## [244] "CMI09"
## [245] "CMI10"
## [246] "CMI11"
## [247] "CMI12"
## [248] "Tmax_wt"
## [249] "Tmax_sp"
## [250] "Tmax_sm"
## [251] "Tmax_at"
## [252] "Tmin_wt"
## [253] "Tmin_sp"
## [254] "Tmin_sm"
## [255] "Tmin_at"
## [256] "Tave_wt"
## [257] "Tave_sp"
## [258] "Tave_sm"
## [259] "Tave_at"
## [260] "PPT_wt"
## [261] "PPT_sp"
## [262] "PPT_sm"
## [263] "PPT_at"
## [264] "Rad_wt"
## [265] "Rad_sp"
## [266] "Rad_sm"
## [267] "Rad_at"
## [268] "DD_0_wt"
## [269] "DD_0_sp"
## [270] "DD_0_sm"
## [271] "DD_0_at"
## [272] "DD5_wt"
## [273] "DD5_sp"
## [274] "DD5_sm"
## [275] "DD5_at"
## [276] "DD_18_wt"
## [277] "DD_18_sp"
## [278] "DD_18_sm"
## [279] "DD_18_at"
## [280] "DD18_wt"
## [281] "DD18_sp"
## [282] "DD18_sm"
## [283] "DD18_at"
## [284] "NFFD_wt"
## [285] "NFFD_sp"
## [286] "NFFD_sm"
## [287] "NFFD_at"
## [288] "PAS_wt"
## [289] "PAS_sp"
## [290] "PAS_sm"
## [291] "PAS_at"
## [292] "Eref_wt"
## [293] "Eref_sp"
## [294] "Eref_sm"
## [295] "Eref_at"
## [296] "CMD_wt"
## [297] "CMD_sp"
## [298] "CMD_sm"
## [299] "CMD_at"
## [300] "RH_wt"
## [301] "RH_sp"
## [302] "RH_sm"
## [303] "RH_at"
## [304] "CMI_wt"
## [305] "CMI_sp"
## [306] "CMI_sm"
## [307] "CMI_at"
## [308] "MAT"
## [309] "MWMT"
## [310] "MCMT"
## [311] "TD"
## [312] "MAP"
## [313] "MSP"
## [314] "AHM"
## [315] "SHM"
## [316] "DD_0"
## [317] "DD5"
## [318] "DD_18"
## [319] "DD18"
## [320] "NFFD"
## [321] "bFFP"
## [322] "eFFP"
## [323] "FFP"
## [324] "PAS"
## [325] "EMT"
## [326] "EXT"
## [327] "MAR"
## [328] "Eref"
## [329] "CMD"
## [330] "RH"
## [331] "CMI"
## [332] "DD1040"## Warning: Removed 36 rows containing non-finite values (stat_boxplot).
Slope
Symptoms
## Warning: Removed 36 rows containing non-finite values (stat_boxplot).
Elevation
Symptoms
## Warning: Removed 36 rows containing non-finite values (stat_boxplot).
Topo & Climate
Slope
CMD
## Warning: Removed 36 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 36 rows containing non-finite values (stat_smooth).
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 36 rows containing non-finite values (stat_smooth).
Elevation
## [1] "field_1" "id" "lat" "long" "el"
## [6] "Aspect" "Profilecurv" "Tangentialc" "Slope" "PNWSRTMDEM"## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 36 rows containing non-finite values (stat_smooth).
Binary Data
## [1] "Healthy" "Unhealthy"Topo
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 36 rows containing non-finite values (stat_smooth).
## Warning: Removed 36 rows containing non-finite values (stat_boxplot).
Climate
Data Exploration
MAT
Symptoms
Site Severity
Size Class
MAP
AHM
SHM
Filtered SHM <200
MSP
Filtered SHM <200
CMD
Filtered SHM <200
Eref
###### Filtered SHM <200
Large Trees on Severe sites
MSP
CMD
Import Soils Data
## [1] "OID_" "field_1"
## [3] "ID2" "lat"
## [5] "long" "el"
## [7] "Aspect" "Profilecurv"
## [9] "Tangentialc" "Slope"
## [11] "PNWSRTMDEM" "RASTERVALU"
## [13] "VAT_MapunitRaster_10m_Count" "VAT_MapunitRaster_10m_MUKEY"
## [15] "muaggatt_OBJECTID" "muaggatt_musym"
## [17] "muaggatt_muname" "muaggatt_mustatus"
## [19] "muaggatt_slopegraddcp" "muaggatt_slopegradwta"
## [21] "muaggatt_brockdepmin" "muaggatt_wtdepannmin"
## [23] "muaggatt_wtdepaprjunmin" "muaggatt_flodfreqdcd"
## [25] "muaggatt_flodfreqmax" "muaggatt_pondfreqprs"
## [27] "muaggatt_aws025wta" "muaggatt_aws050wta"
## [29] "muaggatt_aws0100wta" "muaggatt_aws0150wta"
## [31] "muaggatt_drclassdcd" "muaggatt_drclasswettest"
## [33] "muaggatt_hydgrpdcd" "muaggatt_iccdcd"
## [35] "muaggatt_iccdcdpct" "muaggatt_niccdcd"
## [37] "muaggatt_niccdcdpct" "muaggatt_engdwobdcd"
## [39] "muaggatt_engdwbdcd" "muaggatt_engdwbll"
## [41] "muaggatt_engdwbml" "muaggatt_engstafdcd"
## [43] "muaggatt_engstafll" "muaggatt_engstafml"
## [45] "muaggatt_engsldcd" "muaggatt_engsldcp"
## [47] "muaggatt_englrsdcd" "muaggatt_engcmssdcd"
## [49] "muaggatt_engcmssmp" "muaggatt_urbrecptdcd"
## [51] "muaggatt_urbrecptwta" "muaggatt_forpehrtdcp"
## [53] "muaggatt_hydclprs" "muaggatt_awmmfpwwta"
## [55] "muaggatt_mukey"Merge data
Add consistency to factors
Symptoms
## [1] "Branch Dieback or 'Flagging'"
## [2] "Browning Canopy"
## [3] "Extra Cone Crop"
## [4] "Healthy"
## [5] "Multiple Symptoms (please list in Notes)"
## [6] "New Dead Top (red or brown needles still attached)"
## [7] "Old Dead Top (needles already gone)"
## [8] "Other (please describe in Notes)"
## [9] "Thinning Canopy"
## [10] "Tree is dead"
## [11] "Yellowing Canopy"Unhealthy trees
## [1] "0" "1" "2-3" "4-6" "7-10"
## [6] "More than 10" "Not sure"Tree size
## [1] ""
## [2] "Large (too big to wrap arms around trunk)"
## [3] "Medium (can wrap arms around trunk)"
## [4] "No selection"
## [5] "Other"
## [6] "Small (can wrap hands around trunk)"
## [7] "Very Large (would take many people to wrap arms around trunk)"Filter data
Only include symptoms of interest
## [1] "Healthy"
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"
## [4] "Thinning Canopy"
## [5] "Tree is dead"Only include data with soils data
Only Washington has data currently
Data Exploration
Symptoms
Bedrock Depth
## Warning: Removed 410 rows containing non-finite values (stat_boxplot).
drclasscd
###### drclasswettest 
###### hydgrpdcd 
slopegradwta
## Warning: Removed 20 rows containing non-finite values (stat_boxplot).
niccdcdpct
## Warning: Removed 3 rows containing non-finite values (stat_boxplot).